rs10491650

Variant names:

• chr9-5203054-T-C
• rs10491650

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.296 in 152,052 control chromosomes in the GnomAD database, including 6,787 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.30 (6787 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.22

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.325 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.296 AC: 44997 AN: 151934 Hom.: 6780 Cov.: 32

Gnomad AFR AF: 0.329

Gnomad AMI AF: 0.286

Gnomad AMR AF: 0.284

Gnomad ASJ AF: 0.251

Gnomad EAS AF: 0.257

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.352

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.273

Gnomad OTH AF: 0.291

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.296 AC: 45047 AN: 152052 Hom.: 6787 Cov.: 32 AF XY: 0.301 AC XY: 22363 AN XY: 74342

Gnomad4 AFR AF: 0.330

Gnomad4 AMR AF: 0.284

Gnomad4 ASJ AF: 0.251

Gnomad4 EAS AF: 0.257

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.352

Gnomad4 NFE AF: 0.273

Gnomad4 OTH AF: 0.292

Alfa AF: 0.296 Hom.: 1127

Bravo AF: 0.288

Asia WGS AF: 0.312 AC: 1083 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	0.39
DANN	Benign	0.80

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs10491650; hg19: chr9-5203054; COSMIC: COSV60323497;